/******************************COPYRIGHT NOTICE*******************************/
/*  (c) Centro de Regulacio Genomica                                                        */
/*  and                                                                                     */
/*  Cedric Notredame                                                                        */
/*  12 Aug 2014 - 22:07.                                                                    */
/*All rights reserved.                                                                      */
/*This file is part of T-COFFEE.                                                            */
/*                                                                                          */
/*    T-COFFEE is free software; you can redistribute it and/or modify                      */
/*    it under the terms of the GNU General Public License as published by                  */
/*    the Free Software Foundation; either version 2 of the License, or                     */
/*    (at your option) any later version.                                                   */
/*                                                                                          */
/*    T-COFFEE is distributed in the hope that it will be useful,                           */
/*    but WITHOUT ANY WARRANTY; without even the implied warranty of                        */
/*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                         */
/*    GNU General Public License for more details.                                          */
/*                                                                                          */
/*    You should have received a copy of the GNU General Public License                     */
/*    along with Foobar; if not, write to the Free Software                                 */
/*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
/*...............................................                                           */
/*  If you need some more information                                                       */
/*  cedric.notredame@europe.com                                                             */
/*...............................................                                           */
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/*pair wise aln implementations*/
int myers_miller_pair_wise (Alignment *A, int *ns, int **l_s,Constraint_list *CL);
int diff (Alignment *A, int *ns, int **ls, int s1, int M,int s2, int N , int tb, int te, Constraint_list *CL, int **pos);
int gotoh_pair_wise    (Alignment *A,int*ns, int **l_s,Constraint_list *CL);

int sw_pair_wise (Alignment *A, int gop,int gep, int scale,int*ns, int **l_s,Constraint_list *CL, int maximise );
Alignment ** t_coffee_lalign   (Constraint_list *CL, int scale, int penalty, int maximise,Sequence *S,int sw_t, int sw_l, int sw_z, int *sw_n, int sw_io);


Alignment * get_best_local_aln     ( Alignment *A,Constraint_list *CL,int gop, int gep, int sw_t, int sw_l, int sw_z, int mode);
Alignment *   get_best_ol_local_aln ( Alignment *IN, Constraint_list*CL,int gop, int gep, int sw_t, int sw_l, int sw_z, int mode);
Alignment *  get_best_nol_local_aln ( Alignment *IN, Constraint_list*CL,int gop, int gep, int sw_t, int sw_l, int sw_z, int mode);

int    get_start_point ( Alignment *A,Constraint_list**CL,int gop, int gep, int T, int *first, int *last);

double compute_penalty ( Constraint_list *CL, char *mode, int len);
double compute_scale   ( Constraint_list *CL, char *mode, int len);
int evaluate_penalty (Alignment *A, Constraint_list *CL, int *scale,char *scale_mode, int *penalty, char *penalty_mode, int len_seq); 
Alignment *  add_seq2aln           (Constraint_list *CL,int gop,int gep, Alignment *a_list,int maximise,Sequence  *S, int sw_t, int sw_l, int sw_z, int *sw_n, int sw_io);